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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

Double Penalized Variable Selection Procedure for Partially Linear Models with Longitudinal Data

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Acta Mathematica Sinica,English Series 2014年第11期30卷 1963-1976页

作者： Pei Xin ZHAO An Min TANG Nian Sheng TANG College of Mathematics and statistics Hechi University department of statistics Yunnan University

Based on the double penalized estimation method,a new variable selection procedure is proposed for partially linear models with longitudinal *** proposed procedure can avoid the effects of the nonparametric estimator on the variable selection for the parameters *** some regularity conditions,the rate of convergence and asymptotic normality of the resulting estimators are *** addition,to improve efficiency for regression coefficients,the estimation of the working covariance matrix is involved in the proposed iterative *** simulation studies are carried out to demonstrate that the proposed method performs well.

关键词： Partially linear model variable selection penalized estimation longitudinal data

A one-step implicit iterative method for two finite families of asymptotically nonexpansive mappings in a hyperbolic space

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Applied Mathematics(A Journal of Chinese Universities) 2018年第3期33卷 274-286页

作者： Hafiz Fukhar-ud-din Amna Kalsoom Safeer H Khan department of Mathematics and statistics King Fahd University of Petroleum and Minerals department of Mathematics and statistics International Islamic University department of Mathematics Statistics and Physics Qatar University

We introduce a one-step implicit iterative method for two finite families of asymptotically nonexpansive mappings in a hyperbolic space and use it to approximate common fixed points of these families. The results presented in this paper are new in the setting of hyperbolic spaces. On top, these are generalizations of several results in literature from Banach spaces to hyperbolic spaces. At the end of the paper, we give an example to validate our results.

关键词： uniformly convex hyperbolic space asymptotically nonexpansive mapping common fixed point strong convergence

Estimation and test of restricted linear EV model with nonignorable missing covariates

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Applied Mathematics(A Journal of Chinese Universities) 2018年第3期33卷 344-358页

作者： TANG Lin-jun ZHENG Sheng-chao ZHOU Zhan-gong department of statistics Jiaxing University

This paper deals with estimation and test procedures for restricted linear errors-invariables(EV) models with nonignorable missing covariates. We develop a restricted weighted corrected least squares(WCLS) estimator based on the propensity score, which is fitted by an exponentially tilted likelihood method. The limiting distributions of the proposed estimators are discussed when tilted parameter is known or unknown. To test the validity of the constraints,we construct two test procedures based on corrected residual sum of squares and empirical likelihood method and derive their asymptotic properties. Numerical studies are conducted to examine the finite sample performance of our proposed methods.

关键词： errors-in-variables model nonignorable missing data propensity score smoothed empirical likelihood

Stochastic ordering of medians in exchangeable trivariate normal vectors

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Applied Mathematics(A Journal of Chinese Universities) 2016年第2期31卷 148-156页

作者： Ahad Jamalizadeh Mohsen Madadi Mehdi Amiri N.Balakrishnan department of statistics Faculty of Mathematics & ComputerShahid Bahonar University of Kerman department of statistics Faculty of ScienceHormozgan University department of Mathematics and statistics Mc Master University

In this paper, we establish the stochastic ordering of median from an exchangeable trivaxiate normal vector based on the strength of the correlation coefficient. Specifically, by considering two exchangeable trivariate normal vectors with different correlation coefficients, we show that the absolute value of the median in the vector with smaller correlation coefficient is stochastically smaller than the absolute value of the median in the vector with larger correlation coefficient. We prove this result by utilizing skew-normal distributions.

关键词： Stochastic ordering Exchangeable trivariate normal distribution Order statistics Median Skew-normal distribution 2nd skew-normal distribution.

Optimal Grouping of Heterogeneous Components in Series and Parallel Systems Under Archimedean Copula Dependence

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Journal of Systems Science & Complexity 2022年第3期35卷 1030-1051页

作者： FANG Longxiang ZHANG Xinsheng JIN Qing department of Mathematics and statistics Anhui Normal UniversityWuhu 241000China department of statistics Fudan UniversityShanghai 200433China

This paper considers series and parallel systems comprising n components drawn from a heterogeneous population consisting of m different *** components within each subpopulation are assumed to be dependent,while the subpopulations are independent of each *** authors also assume that the subpopulations have different Archimedean copulas for their *** this setup,the authors discuss the series and parallel systems reliability for three different cases,*** authors use the theory of stochastic orders and majorization to establish the main results,and finally present some numerical examples to illustrate all the results established here.

关键词： Archimedean copula majorization parallel system reliability Schur-convex/concave function series system stochastic orders

Slip effects on streamline topologies and their bifurcations for peristaltic flows of a viscous fluid

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Chinese Physics B 2014年第6期23卷 341-352页

作者： Z.Asghar N.Ali department of Mathematics and statistics International Islamic University

We discuss the effects of the surface slip on streamline patterns and their bifurcations for the peristaltic transport of a Newtonian fluid. The flow is in a two-dimensional symmetric channel or an axisymmetric tube. An exact expression for the stream function is obtained in the wave frame under the assumptions of long wavelength and low Reynolds number for both cases. For the discussion of the particle path in the wave frame, a system of nonlinear autonomous differential equations is established and the methods of dynamical systems are used to discuss the local bifurcations and their topological changes. Moreover, all types of bifurcations and their topological changes are discussed graphically. Finally, the global bifurcation diagram is used to summarize the bifurcations.

关键词： viscous fluid slip condition streamline topologies bifurcation

Efficient Asymmetrical Extended Designs Under Wrap-Around L2-Discrepancy

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Journal of Systems Science & Complexity 2018年第5期31卷 1391-1404页

作者： GOU Tingxun QIN Hong CHATTERJEE Kashinath department of statistics Central China Normal University Wuhan 430079 China department of statistics Visva-Bharati University Santiniketan India

The purpose of the present article is to introduce a class of mixed two- and three-level extended designs obtained by adding some new runs to an existing mixed two- and three-level design. A formulation of wrap-around L2-discrepancy for the extended designs is developed. As a benchmark of obtaining （nearly） uniform asymmetrical extended designs, a lower bound to the wrap-around L2- discrepancy for our proposed designs is established. Thorough numerical results are displayed, which provide further corroboration to the derived theoretical results.

关键词： Asymmetrical extended design follow-up experiment lower bound wrap-around L2-discrepancy.

Stabilities of delay stochastic McKean-Vlasov equations in the G-framework

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Science China(Information Sciences) 2025年第1期 255-277页

作者： Haiyan YUAN Quanxin ZHU department of Mathematics Heilongjiang Institute of Technology Key Laboratory of Computing and Stochastic Mathematics (Ministry of Education) School of Mathematics and Statistics Hunan Normal University

This article focuses on a type of stochastic Mc Kean-Vlasov equation in the G-framework(G-SMVE) and addresses the stability issue for delay stochastic Mc Kean-Vlasov equations in the G-framework(G-SMVDEs). Distribution dependence and uncertainty prevent us from directly applying the stochastic analysis method for stochastic Mc Kean-Vlasov equations(SMVEs)to G-SMVEs directly. To overcome this difficulty, we introduce definitions, including the derivative of a function with a law under the G-expectation and the Lions derivatives. Then we construct a new G-It? formula for G-SMVEs according to the G-It? formula for stochastic differential equations in the G-framework(G-SDEs) and the It? formula for SMVEs. Using the new G-It? formula and the Lyapunov functional method, we investigate the moment exponential stability and almost sure asymptotic stability of G-SMVDEs. To overcome the difficulty in obtaining the distribution dependence of the exact solution to the G-SMVDE, we introduce the empirical measure and the corresponding interacting particle system, and then prove the stability equivalence between the underlying G-SMVDE and the corresponding interacting particle system. Two examples are used to confirm our theoretical results.

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